NPASS Compound

Natural Product: NPC205467

Natural Product ID	NPC205467
Common Name ? The InCHIKey will be temporarily assigned as the "Common Name" if no IUPAC name or alternative short name is available.	ALEUBOFIDHNMTA-UHFFFAOYSA-N
IUPAC Name	n.a.
Synonyms
Synthetic Gene Cluster	n.a.
ChEMBL Identifier	n.a.
PubChem CID	14237668
Chemical Classification	CHEMONTID:0000000 [Organic compounds] [CHEMONTID:0000261] Phenylpropanoids and polyketides [CHEMONTID:0002506] Isoflavonoids [CHEMONTID:0001612] Isoflavans [CHEMONTID:0001827] Isoflavanones [CHEMONTID:0003526] 6-prenylated isoflavanones

The Chemical Classification was calculated by Classyfire, a software for chemical taxonomy calculation. Reference: DOI:10.1186/s13321-016-0174-y.

Chemical Representations

RDKit 3D 57 59 0 0 0 0 0 0 0 0999 V2000 8.4951 1.5039 -0.8144 C 0 0 0 0 0 0 0 0 0 0 0 0 7.6646 0.3486 -0.3056 C 0 0 0 0 0 0 0 0 0 0 0 0 6.4290 0.2135 -0.7501 C 0 0 0 0 0 0 0 0 0 0 0 0 5.4993 -0.8554 -0.3505 C 0 0 0 0 0 0 0 0 0 0 0 0 4.2526 -0.3364 0.2872 C 0 0 0 0 0 0 0 0 0 0 0 0 3.0431 -0.2939 -0.3865 C 0 0 0 0 0 0 0 0 0 0 0 0 1.8813 0.1872 0.2021 C 0 0 0 0 0 0 0 0 0 0 0 0 1.9879 0.6271 1.5064 C 0 0 0 0 0 0 0 0 0 0 0 0 3.1971 0.5933 2.2043 C 0 0 0 0 0 0 0 0 0 0 0 0 4.3336 0.1085 1.5887 C 0 0 0 0 0 0 0 0 0 0 0 0 5.5616 0.0619 2.2620 O 0 0 0 0 0 0 0 0 0 0 0 0 0.6179 0.2240 -0.5266 C 0 0 0 0 0 0 0 0 0 0 0 0 0.5650 0.6876 -1.8255 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5730 0.7218 -2.4823 O 0 0 0 0 0 0 0 0 0 0 0 0 -1.7201 0.3277 -1.9683 C 0 0 0 0 0 0 0 0 0 0 0 0 -2.8999 0.3718 -2.6716 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.0901 -0.0517 -2.0960 C 0 0 0 0 0 0 0 0 0 0 0 0 -4.1374 -0.5275 -0.8108 C 0 0 0 0 0 0 0 0 0 0 0 0 -5.4097 -0.9854 -0.1524 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.1612 0.2533 0.2638 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.4409 -0.1082 0.9310 C 0 0 0 0 0 0 0 0 0 0 0 0 -7.7579 -1.3807 1.0936 C 0 0 0 0 0 0 0 0 0 0 0 0 -8.3730 0.9569 1.4239 C 0 0 0 0 0 0 0 0 0 0 0 0 -6.3420 1.1494 -0.7654 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9423 -0.5678 -0.1116 C 0 0 0 0 0 0 0 0 0 0 0 0 -1.7566 -0.1500 -0.6755 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5834 -0.1968 0.0332 C 0 0 0 0 0 0 0 0 0 0 0 0 -0.5886 -0.6272 1.2097 O 0 0 0 0 0 0 0 0 0 0 0 0 -2.9393 -1.0438 1.1973 O 0 0 0 0 0 0 0 0 0 0 0 0 -5.2631 0.0080 -2.8432 O 0 0 0 0 0 0 0 0 0 0 0 0 8.3259 -0.5367 0.6551 C 0 0 0 0 0 0 0 0 0 0 0 0 9.0200 1.9785 0.0509 H 0 0 0 0 0 0 0 0 0 0 0 0 9.2683 1.0473 -1.4780 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8889 2.2068 -1.4001 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0266 0.9308 -1.4727 H 0 0 0 0 0 0 0 0 0 0 0 0 5.1622 -1.3733 -1.2978 H 0 0 0 0 0 0 0 0 0 0 0 0 5.9028 -1.6409 0.2800 H 0 0 0 0 0 0 0 0 0 0 0 0 2.9865 -0.6452 -1.4084 H 0 0 0 0 0 0 0 0 0 0 0 0 1.0890 1.0113 1.9966 H 0 0 0 0 0 0 0 0 0 0 0 0 3.2613 0.9423 3.2234 H 0 0 0 0 0 0 0 0 0 0 0 0 6.0236 -0.8062 2.4217 H 0 0 0 0 0 0 0 0 0 0 0 0 1.5015 1.0218 -2.2789 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.8900 0.7466 -3.6983 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.1261 -1.5644 0.7377 H 0 0 0 0 0 0 0 0 0 0 0 0 -6.0159 -1.5792 -0.8777 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.5196 0.7843 1.0230 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.7064 -1.6351 1.5875 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.0777 -2.1369 0.7404 H 0 0 0 0 0 0 0 0 0 0 0 0 -9.1800 1.1467 0.6981 H 0 0 0 0 0 0 0 0 0 0 0 0 -8.8463 0.5732 2.3531 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.8033 1.8535 1.7073 H 0 0 0 0 0 0 0 0 0 0 0 0 -7.2845 1.3900 -0.9373 H 0 0 0 0 0 0 0 0 0 0 0 0 -2.5243 -1.9460 1.3927 H 0 0 0 0 0 0 0 0 0 0 0 0 -5.6593 -0.8355 -3.2409 H 0 0 0 0 0 0 0 0 0 0 0 0 7.8326 -1.4738 0.8889 H 0 0 0 0 0 0 0 0 0 0 0 0 8.4178 0.0196 1.6356 H 0 0 0 0 0 0 0 0 0 0 0 0 9.3766 -0.6998 0.2807 H 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 2 3 2 3 3 4 1 0 4 5 1 0 5 6 2 0 6 7 1 0 7 8 2 0 8 9 1 0 9 10 2 0 10 11 1 0 7 12 1 0 12 13 2 0 13 14 1 0 14 15 1 0 15 16 2 0 16 17 1 0 17 18 2 0 18 19 1 0 19 20 1 0 20 21 1 0 21 22 2 0 21 23 1 0 20 24 1 0 18 25 1 0 25 26 2 0 26 27 1 0 27 28 2 0 25 29 1 0 17 30 1 0 2 31 1 0 10 5 1 0 27 12 1 0 26 15 1 0 1 32 1 0 1 33 1 0 1 34 1 0 3 35 1 0 4 36 1 0 4 37 1 0 6 38 1 0 8 39 1 0 9 40 1 0 11 41 1 0 13 42 1 0 16 43 1 0 19 44 1 0 19 45 1 0 20 46 1 0 22 47 1 0 22 48 1 0 23 49 1 0 23 50 1 0 23 51 1 0 24 52 1 0 29 53 1 0 30 54 1 0 31 55 1 0 31 56 1 0 31 57 1 0 M END

Standard InCHIKey	ALEUBOFIDHNMTA-UHFFFAOYSA-N
Standard InCHI	InChI=1S/C25H26O6/c1-13(2)5-6-16-9-15(7-8-19(16)26)18-12-31-22-11-21(28)17(10-20(27)14(3)4)24(29)23(22)25(18)30/h5,7-9,11-12,20,26-29H,3,6,10H2,1-2,4H3
SMILES	CC(=CCc1cc(ccc1O)c1coc2cc(c(CC(C(=C)C)O)c(c2c1=O)O)O)C

Calculated Properties

Physi-Chem Properties

Molecular Weight:	422.17	Volume:	441.663 ? Van der Waals volume.
Dense:	0.956	LogP:	3.927 ? The logarithm of the n-octanol/water distribution coefficients.
logD7.4:	3.052 ? The logarithm of the n-octanol/water distribution coefficient at pH=7.4.	LogS:	-4.537 ? The logarithm of aqueous solubility value.
Rotatable Bonds:	6.0	Rigid Bonds:	20.0
TPSA:	111.13 ? Topological Polar Surface Area.	H-Bond Acceptor:	6.0
H-Bond Donor:	4.0	Rings:	3.0
Heavy Atoms:	6.0

MedChem Properties

QED Drug-Likeness Score:	0.433	GASA:	0.0 ? GASA represents the probability of being difficult to synthesize, ranging from 0 to 1.
Synthetic Accessibility Score:	3.573	Fsp³:	0.24
MCE-18:	44.0 ? MCE-18 stands for medicinal chemistry evolution.MCE-18≥45 is considered a suitable value.	Lipinski Rule-of-5:	Rejected
Pfizer Rule:	Rejected	GSK Rule:	Accepted
Golden Triangle Rule:	Rejected	BMS Rule:	0
Chelating Alert:	0	PAINS Alert:	0
Colloidal aggregators:	0.802	Fluc inhibitor:	0.311 ? The fluc inhibitor value is the probability of being fLuc inhibitors, within the range of 0 to 1.
Blue fluorescence:	0.944 ? The blue fluorescence value is the probability of being blue fluorescence, within the range of 0 to 1	Green fluorescence:	0.483 ? The green fluorescence value is the probability of being green fluorescence, within the range of 0 to 1
Reactive compounds:	0.184	Promiscuous compounds:	0.094

ADMET Properties (ADMETlab3.0)

ADMET: Absorption

Caco-2 Permeability:	-5.014	MDCK Permeability:	-4.63
Pgp-inhibitor:	0.001	Pgp-substrate:	0.019
PAMPA:	0.968 ? The experimental data for Peff was logarithmically transformed (logPeff). Molecules with log Peff values below 2.0 were classified as low-permeability (Category 0), while those with log Peff values exceeding 2.5 were classified as high-permeability (Category 1).	Human Intestinal Absorption (HIA):	0.131
20% Bioavailability (F20%):	0.988	30% Bioavailability (F30%):	1.0
50% Bioavailability (F50%):	1.0

ADMET: Distribution

Blood-Brain-Barrier Penetration (BBB):	0.0	MRP1:	0.801
Plasma Protein Binding (PPB):	94.517%	Volume Distribution (VD):	0.416
Fu:	5.634% ? The fraction unbound in plasms.	OATP1B1 inhibitor:	0.344
OATP1B3 inhibitor:	0.971	BCRP inhibitor:	0.929
BSEP inhibitor:	0.292

ADMET: Metabolism

CYP1A2-inhibitor:	0.295	CYP1A2-substrate:	1.0
CYP2C19-inhibitor:	0.346	CYP2C19-substrate:	0.889
CYP2C9-inhibitor:	0.279	CYP2C9-substrate:	0.024
CYP2D6-inhibitor:	0.711	CYP2D6-substrate:	0.207
CYP3A4-inhibitor:	0.002	CYP3A4-substrate:	1.0
CYP2B6-substrate:	0.0	CYP2C8-inhibitor:	1.0
HLM stability:	1.0 ? Human liver microsomal (HLM) stability. Category 0: stable+ (HLM > 30 min); Category 1: unstable- (HLM ≤ 30 min). The output value is the probability of human liver microsomal instability, where a value closer to 1 indicates a higher likelihood of instability.

ADMET: Excretion

Clearance (CL):

8.89

Half-life (T1/2):

1.099

ADMET: Toxicity

hERG Blockers:	0.06	hERG Blockers (10um):	0.542
Human Hepatotoxicity (H-HT):	0.578	Drug-induced Liver Injury (DILI):	0.485
AMES Toxicity:	0.492	Rat Oral Acute Toxicity:	0.671
Maximum Recommended Daily Dose:	0.812	Skin Sensitization:	0.812
Carcinogencity:	0.546	Eye Corrosion:	0.0
Eye Irritation:	0.816	Respiratory Toxicity:	0.917
Drug-induced Neurotoxicity:	0.344	Ototoxicity:	0.708
Hematotoxicity:	0.116	Drug-induced Nephrotoxicity:	0.453
Genotoxicity:	0.932	RPMI-8226 Immunitoxicity:	0.095
A549 Cytotoxicity:	0.233	Hek293 Cytotoxicity:	0.378
BCF:	1.719 ? Bioconcentration factors are used for considering secondary poisoning potential and assessing risks to human health via the food chain. The unit is -log10[(mg/L)/(1000*MW)].	IGC50:	4.676 ? 48 hour Tetrahymena pyriformis IGC50. The unit of IGC50 is -log10[(mg/L)/(1000*MW)].
LC50DM:	6.106 ? 48 hour Daphnia magna LC50. The unit of LC50DM is -log10[(mg/L)/(1000*MW)].	LC50FM:	5.574 ? 96 hour fathead minnow LC50. The unit of LC50FM is -log10[(mg/L)/(1000*MW)].

Species Source

Organism ID	Organism Name	Taxonomy Level	Family	SuperKingdom	Isolation Part	Collection Location	Collection Time	Reference
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	stem	n.a.	DOI[10.1016/S0031-9422(99)00103-X]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[19969457]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	PMID[21314138]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[COCONUT]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[HerDing]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[TCMID]
NPO27553	Derris scandens	Species	Fabaceae	Eukaryota	n.a.	n.a.	n.a.	Database[UNPD]

Note for Reference:
In addition to directly collecting NP source organism data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated them from below databases:
☉ UNPD: Universal Natural Products Database [PMID: 23638153].
☉ StreptomeDB: a database of streptomycetes natural products [PMID: 33051671].
☉ TM-MC: a database of medicinal materials and chemical compounds in Northeast Asian traditional medicine [PMID: 26156871].
☉ TCM@Taiwan: a Traditional Chinese Medicine database [PMID: 21253603].
☉ TCMID: a Traditional Chinese Medicine database [PMID: 29106634].
☉ TCMSP: The traditional Chinese medicine systems pharmacology database and analysis platform [PMID: 24735618].
☉ HerDing: a herb recommendation system to treat diseases using genes and chemicals [PMID: 26980517].
☉ MetaboLights: a metabolomics database [PMID: 27010336].
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

NP Quantity Composition/Concentration

Organism ID	Organism Name	Organism Material Preparation	Organism Part	NP Quantity (Standard)	NP Quantity (Minimum)	NP Quantity (Maximum)	Quantity Unit	Reference

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP quantitative records for specific NP domains (e.g., NPS from foods or herbs) from domain-specific databases. These databases include:
☉ DUKE: Dr. Duke's Phytochemical and Ethnobotanical Databases.
☉ PHENOL EXPLORER: is the first comprehensive database on polyphenol content in foods [PMID: 24103452], its homepage can be accessed at here.
☉ FooDB: a database of constituents, chemistry and biology of food species [www.foodb.ca].

Biological Activity

Molecular-level activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vitro activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

In vivo activity

Target ID	Target Type	Target Name	Target Organism	Activity Type	Activity Relation	Value	Unit	Reference

Experimental ADME

Experiment Model	Experiment Tissue	ADME Type	ADME Relation	ADME Value	ADME Unit	Reference

Experimental Toxicity

Quantitative toxicity

Experiment Model	Experiment Organism	Toxicity Type	Toxicity Relation	Toxicity Value	Toxicity Unit	Reference

Common Abbreviations:
LC: Lethal Concentration; LD: Lethal Dose; LT:Lethal Time; NOAEL: No-observed-adverse-effect Level; BMDL: Benchmark Dose Lower Confidence Limit; BMD: Benchmark Dose; BMC:Benchmark Concentration; LOAEL: Lowest Observed Adverse Effect Level; RfD:Reference Dose; RfC:Reference Concentration; MRL: Minimal Risk Level; MEG: Maximum Exposure Guideline; PAC: Protective Action Criteria

Categorical toxicity labels

Hepatotoxicity	Carcinogenicity	Mutagenicity	Cardiotoxicity	Respiratory Toxicity	Eye Irritation	Endocrine Disruption

Note for Reference:
In addition to directly collecting NP quantitative data from primary literature (where reference will provided as NCBI PMID or DOI links), NPASS also integrated NP toxicity records from domain-specific databases. These databases include:
☉ ToxValDB: a curated database that compiles quantitative toxicity values for chemicals from diverse public sources to support toxicological research and risk assessment.
☉ TOXRIC: a comprehensive, free-to-access, online database providing toxicological/feature data. The toxicity labels are retrieved from this database. [PMID: 36400569]

Chemically structural similarity

Similar Active Natural Products in NPASS

Top-200 similar NPs were calculated against the active-NP-set (includes approximately 50,000 NPs with experimentally-derived bioactivity available in NPASS)

Similarity is measured using the Tanimoto coefficient (Tc) , which compares the binary fingerprints of two molecules. Tc is calculated as the intersection divided by the union of '1' bits in the fingerprints, ranging from 0 to 1, with 1 indicating highest similarity.

● The left chart: Distribution of similarity level between NPC205467 and all remaining natural products in the NPASS database.
● The right table: Most similar natural products (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	21217
0.1-0.2	26033
0.2-0.3	2182
0.3-0.4	326
0.4-0.5	69
0.5-0.6	18
0.6-0.7	8
0.7-0.8	0
0.8-0.85	1
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Natural Product ID
0.8308	Intermediate Similarity	NPC48624
0.7143	Intermediate Similarity	NPC475705
0.7101	Intermediate Similarity	NPC213659
0.7101	Intermediate Similarity	NPC326109
0.6712	Remote Similarity	NPC476178
0.6667	Remote Similarity	NPC259166
0.662	Remote Similarity	NPC203077
0.6571	Remote Similarity	NPC20472
0.625	Remote Similarity	NPC51070
0.6164	Remote Similarity	NPC215311
0.6111	Remote Similarity	NPC55832
0.6081	Remote Similarity	NPC80962
0.5974	Remote Similarity	NPC117836
0.5897	Remote Similarity	NPC323626
0.5867	Remote Similarity	NPC40942
0.5769	Remote Similarity	NPC51887
0.5733	Remote Similarity	NPC268204
0.5698	Remote Similarity	NPC324447
0.5696	Remote Similarity	NPC324233
0.56	Remote Similarity	NPC482730
0.5595	Remote Similarity	NPC302762
0.5526	Remote Similarity	NPC172250
0.5395	Remote Similarity	NPC238279
0.5325	Remote Similarity	NPC232947
0.5301	Remote Similarity	NPC123653
0.5294	Remote Similarity	NPC278968
0.5128	Remote Similarity	NPC59210
0.5128	Remote Similarity	NPC270708
0.5125	Remote Similarity	NPC134287
0.5063	Remote Similarity	NPC219917

Similar Clinical/Approved Drugs

Similarity level is defined by Tanimoto coefficient (Tc) between two molecules.

● The left chart: Distribution of similarity level between NPC205467 and all drugs/candidates.
● The right table: Most similar clinical/approved drugs (Tc>=0.5 or Top200).

range	Tanimoto Coefficient
0-0.1	4254
0.1-0.2	4866
0.2-0.3	27
0.3-0.4	2
0.4-0.5	1
0.5-0.6	0
0.6-0.7	0
0.7-0.8	0
0.8-0.85	0
0.85-0.9	0
0.9-0.95	0
0.95-1	0

Similarity Score	Similarity Level	Drug ID	Developmental Stage
		NPD

Bioactivity similarity

Similar Natural Products in NPASS

Similarity level is defined by Bioactivity similarity was calculated based on bioactivity descriptors of compounds. The bioactivity descriptors were calculated by a recently developed AI algorithm Chemical Checker (CC) [Nature Biotechnology, 38:1087–1096, 2020; Nature Communications, 12:3932, 2021], which evaluated bioactivity similarities at five levels:
☉ A: chemistry similarity;
☉ B: biological targets similarity;
☉ C: networks similarity;
☉ D: cell-based bioactivity similarity;
☉ E: similarity based on clinical data.
Those 5 categories of CC bioactivity descriptors were calculated and then subjected to manifold projection using UMAP algorithm, to project all NPs on a 2-Dimensional space. The current NP was highlighted with a small circle in the 2-D map. Below figures: left-to-right, A-to-E.

A: chemistry similarity

B: biological targets similarity

C: networks similarity

D: cell-based bioactivity similarity

E: similarity based on clinical data